dna sequencing - protocol for pulldown of DNA breakpoints?

The paper you cite says that the break points are single stranded DNA which have specific proteins bound to them.

I'm not an expert here, but if thats the cause of meitotic break points there are some interesting possibilities for detecting them:

you could detect them with a tiling array. - that's an micro array which has an oligomer every 40 bp or so of the genome. The array could be used in a CHP experiment that detects the same proteins as in this paper.

Its possible that the array could possibly hybridize the single stranded DNA from the genome too if the conditions were right. This sounds noisy though.

On the cheap side it might be possible to use PCR to copy the single stranded DNA from a chromosomal DNA prep. if the oligos you use are labelled with streptavidin say, you could isolate it , re amplify it and sequence cheaply.

any of these sound like a good bit of work :)